RetrogeneDB ID: retro_btau_1830

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:80989753..80990731(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSBTAG00000012225
• Aliases: None
• Description: importin subunit alpha-2 [Source:RefSeq peptide;Acc:NP_001029621]

Sequence

>retro_btau_1830
GGTGCAGTTGATCCGCTATTGGCACTTCTGGTTGTCCCTGATATGTCATCTCTAGTATGTGGTTACTTACGCAGTCTTAC
CTGGACACTTTCAAATCTTTGTCCCAACAAGAATCCTGCACCCCTCTTAGAGGCTATTGAGCAGATTCTTCCTACTTTAA
TTCATCTCCTACATCACGATGATCCAGAAGTATTAGCTGATACCTGCTGGGCTATTTCCTACCTTACTGGTGGTCCAAAT
GAATGGATTGAAATGATTGTGAAAACTGGGGTTGTACCCCAACTTGTGAAGCTTTTAGGAGCTACTGAATTGCCAGTTGT
GACTCCTGTGCTCAGAGCCACAGGAAATATTGTCACTGGGACACATGAACAAACACAGGTTGTAATAGATGCAGGAGCAC
TTGCTGTATTTCCCAGCCTGCTGACAAACTCCAAAACTAATATTCAGAAGGAAGCTACGTGGACAATGTCAAACATCTCA
GCTGGCCGCCAGCACCAGATACAACAAGTTGTGAATCATGGATTAGTCCCATTCCTTGTTGGCCTTCTCTCAAAGACAGA
CTTTAAGACATAAAAGGAAGCCACATGGGCTGTGAATAACTATACAAGTGGAGGAACTGTTGAGCAGATCGTGTACCTTG
TTCATTGTGGCATAATAGAGCTGTTGATGAACCTCCTAACTGCAAAAGATACCAAAATTGGTCTGGTTATTCTGGATGCC
ATTTCAAATATCTTTTGGGCTGCTGAGAAACTAGGTGAAACTGAGAAACTTAGTATAATGATTGAAGAATGTAGAGGTTT
GGACAAAATTGAAGCTCTACAAAACCATGAAAATGAGTCTGTGTACAAAGCTTCATTAAACTTAATCGAGAAGTATTTCT
TTGTAGAGGAAGAGGAAGATCAAAATGTTGTGCCAGAAACTACCTCTGAAGGCTATACATTCCAAGTGCAGGATGGCTCT
GCTGGGACCTTCAACTTT

Alignment

ORF - retro_btau_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLEAIEQILPTLVRLLHHDDPEVLADTCW
          GAVDPLLALL.VPDMSSL.CGYLR.LTWTLSNLC.NKNPAP.LEAIEQILPTL..LLHHDDPEVLADTCW
Retrocopy GAVDPLLALLVVPDMSSLVCGYLRSLTWTLSNLCPNKNPAPLLEAIEQILPTLIHLLHHDDPEVLADTCW

Parental  AISYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSL
          AISYLT.GPNE.IEM.VKTGVVPQLVKLLGATELP.VTP.LRA.GNIVTGT.EQTQVVIDAGALAVFPSL
Retrocopy AISYLTGGPNEWIEMIVKTGVVPQLVKLLGATELPVVTPVLRATGNIVTGTHEQTQVVIDAGALAVFPSL

Parental  LTNSKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGLLSKADFKTQKEAAWAVNNYTSGGTVEQI
          LTNSKTNIQKEATWTMSNI.AGRQ.QIQQVVNHGLVPFLVGLLSK.DFKT.KEA.WAVNNYTSGGTVEQI
Retrocopy LTNSKTNIQKEATWTMSNISAGRQHQIQQVVNHGLVPFLVGLLSKTDFKT*KEATWAVNNYTSGGTVEQI

Parental  VYLVHCGIIEPLMNLLTAKDTKIVLVILDAVSNIFRAAEKLGETEKLGIMIEECGGLDKIEALQNHENES
          VYLVHCGIIE.LMNLLTAKDTKI.LVILDA.SNIF.AAEKLGETEKL.IMIEEC.GLDKIEALQNHENES
Retrocopy VYLVHCGIIELLMNLLTAKDTKIGLVILDAISNIFWAAEKLGETEKLSIMIEECRGLDKIEALQNHENES

Parental  VYKASLNLIEKYFSVEEEEDQNVVPETTSEGYTFRVQDGSAGTFSF
          VYKASLNLIEKYF.VEEEEDQNVVPETTSEGYTF.VQDGSAGTF.F
Retrocopy VYKASLNLIEKYFFVEEEEDQNVVPETTSEGYTFQVQDGSAGTFNF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	10.89 RPM
ERP005899_muscle	0.00 RPM	56.96 RPM
SRP017611_brain	0.14 RPM	19.41 RPM
SRP017611_kidney	0.12 RPM	26.02 RPM
SRP017611_liver	0.00 RPM	12.46 RPM
SRP030211_testis	0.27 RPM	438.79 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1830 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1830 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000004850	1 retrocopy	retro_btau_1842,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830 ,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,